I agree with the commenters who suggest that you may be a little low on pubs for some of the competitive medical centers. I applied very similarly to mostly AMCs based on fit and my career goals and have been really shocked by just how competitive it is. I have 9 publications (3 first author, with 3 more first author pubs under review), an F31, and about 2,500 clinical hours so I thought I would be fairly competitive, but have only had about a 50% hit rate for interviews. I'm definitely not complaining because I am happy with the interviews that I have gotten, but it's crazy how competitive it is! Also, there is someone in my program with (no joke) about 4,000 clinical hours (and otherwise a good vita, too) who has only gotten two interviews so far.
I also strongly suggest maybe emailing your top site or two to ask for feedback on your application. They don't have to give you the feedback, but many of them will. I asked one of the sites where I didn't get an interview for feedback and got some that was very helpful and I know a couple other people in my program have done the same. Also, as far as competitiveness, remember it varies considerably by track. For instance, University of Chicago may interview 60 or so applicant, but I know that the Eating Disorder track only interviews about 10 or less for that one slot.
I'm really sorry that this process has been such a struggle. All I can say is that it is a terrible, terrible process. I am sure you are a fabulous applicant; it's just the distinctions between the fabulous applicant who gets an interview and the one that does not are so fine. I think the best you can do right now is focus on preparing for the interview(s) you get (I also know a number of people who have matched with one or two interviews!) and maybe seek feedback so that you can know how to strengthen yourself or your search for (god forbid!) next year if you need to repeat the process or else (hopefully!) next year for applying to postdocs. Also a positive note: I have heard the postdoc process to be far more humane and less competitive.